SEOUL—Samsung Group heir apparent Lee Jae-yong on Friday got what he wanted: a combination of two affiliates that strengthens his hold on the world’s biggest smartphone maker,
Samsung
Electronics Co.

Now comes the hard part.

In the coming months, the 47-year-old Harvard-educated Mr. Lee faces a formidable task list as he attempts to repair the reputation of the
Samsung
conglomerate after a bruising six-week shareholder proxy battle with U.S. hedge fund Elliott Associates LP.

Mr. Lee will have to mollify restive shareholders—including Elliott—by improving corporate governance and boosting shareholder returns at the newly merged entity, a de facto group holding company in which he will hold a direct 16.5% stake.

Mr. Lee, whose father’s infirmity has thrust him forward, also will have to protect his family’s empire from further attacks by Elliott as well as other hedge funds. In addition, he must deal with broader public sentiment toward the country’s sprawling conglomerates—known as chaebol in Korean—that are often criticized for putting family interests ahead of shareholders.

Ahead of Friday’s shareholder vote, in which Samsung won a slim victory for an $8 billion merger of
Cheil Industries Inc.
and
Samsung C&T Corp.
, Grace Jeon, a small shareholder of both companies, said she opposed the deal. “This merger is for Lee Jae-yong, by Lee Jae-yong and of Lee Jae-yong,” the 53-year-old resident of the city of Ilsan said.

The immediate concern for Mr. Lee will be to neutralize Elliott and its founder, Paul Singer, who have developed a reputation picking outsize fights in often inhospitable markets. The New York-based hedge fund, which as of now would be a key shareholder in the merged Samsung companies, is perhaps best known for its yearslong battle with the government of Argentina over debt the country defaulted on in 2001.

Elliot, holding a 7.1% stake in Samsung C&T, has sought to invalidate the merger in the courts, and earlier in the week took its case to South Korea’s Supreme Court. Separately, Elliott has accumulated 1% stakes in two Samsung affiliates with holdings in Samsung C&T, and could use those positions to bring legal action against company directors for failing to carry out their duties on behalf of minority shareholders, people familiar with the matter said.

“Elliott is disappointed that the takeover appears to have been approved against the wishes of so many independent shareholders and reserves all options at its disposal,” an Elliott spokesman said after the shareholder vote.

To counter Elliott’s moves, Mr. Lee will have to show that he is taking corporate governance seriously. As South Korea’s largest chaebol, Samsung has long drawn criticism from global investors for what they characterize as the company’s opaque decision-making, convoluted cross-holdings and pliant outside directors.

As Elliott’s activism appeared to threaten the merger’s passage, Samsung’s executives pledged last month to set up an independent corporate governance body and boost dividends once the deal was approved—a promise that Elliott said “merely serves to lay bare the total disregard with which they have treated minority shareholders.”

Samsung’s controlling Lee family scored a victory Friday over U.S. hedge fund Elliott Associates. The WSJ’s Yun-Hee Kim discusses what happened at the shareholder meeting and what could be next. Photo: Reuters

That scrutiny will surely persist after the merger. Hours after shareholders approved the deal, civic groups skeptical of the chaebols’ influence issued a statement expressing disappointment with the outcome.

“Without Samsung Group making changes, there will be no change to Korea’s economy,” according to a statement from People’s Solidarity for Participatory Democracy.

“Without Samsung’s owner family making changes, there will be no change to Korea’s society.”

The pressure for change applied by the likes of Elliott could be blunted. Some South Korean business leaders and legislators have begun to call for U.S.-style dual-class ownership structures and so-called poison pills to fend off attacks from foreign hedge funds.

Meanwhile, Mr. Lee must work to meet the market’s lofty expectations for the newly merged company’s growth, which Samsung says will come from synergies in the construction business and a big bet on biopharmaceuticals—a business close to Mr. Lee’s heart, according to people familiar with the matter.

Before the merger, shares in the acquiring company Cheil Industries, which is 23%-owned by Mr. Lee, commanded a share price more than 100 times future projected earnings—an eye-popping premium that analysts chalk up to a belief among investors that aligning with Mr. Lee’s interests would be a good bet.

Samsung now faces the challenge of turning its fledgling biopharmaceutical business, which is housed in affiliate companies owned by Cheil Industries and Samsung Electronics, into a money spinner, analysts say.

More broadly, observers say Samsung’s leadership will have to devote time and effort to show that it will follow through on its pledges to boost shareholder rights prior to a further restructuring of the conglomerate’s roughly 70 companies.

“Meeting global standards is about a lot of different things, including protecting the rights of outside and minority shareholders, but these have been ignored,” said Ryu Young-jae, chief executive of Sustinvest Inc., a Seoul-based proxy-advisory firm that recommended users block the merger.

It doesn’t help that, inside and outside Samsung, Mr. Lee’s involvement in business decisions is relatively unknown, raising questions about his readiness to run South Korea’s largest conglomerate. A spokesman for Samsung Group declined to make Mr. Lee available for comment.

One of his first public moves came in 2000, when an Internet-related venture that he started, called eSamsung, racked up losses after the Internet bubble burst. For the most part, he cut a low profile over the next decade—which included stints as chief customer officer and chief operating officer at Samsung Electronics—and limited his public presence to scripted events. In 2012, he became vice chairman of Samsung Electronics, which itself is facing intensified competition in the smartphone market.

Lately, he has stepped up his public appearances, serving as the face of Samsung in meetings with Facebook Inc.’s Mark Zuckerberg, Google Inc.’s Larry Page and Chinese President Xi Jinping.

After a deadly outbreak last month of the Middle East respiratory syndrome known as the MERS virus—centered at the Samsung Medical Center, where his father occupies a VIP hospital room following a heart attack—the younger Mr. Lee bowed in apology before reporters as the hospital drew criticism for its role in spreading MERS.

“We have failed to live up to the expectations of the public,” he said.

Friday’s merger approval is likely to focus the spotlight more directly on Mr. Lee.

“Lee Jae-yong is being tested now,” said Kim Sang-jo, an economics professor at Hansung University and the outspoken director of a prominent civic group that opposed the deal.